Carbon biogeochemistry of a tropical ecosystem (The Cochin Estuary, India) undergoing increased human intervention was studied during February (premonsoon), April (early monsoon) and September (monsoon) 2005. The Cochin estuary sustains high levels of pCO2 (up to 6000 latm) and CO2 effluxes (up to 274 mmolC m-2 d-1) especially during monsoon. A first-order estimate of the carbon mass balance shows that net production of dissolved inorganic carbon is an order of magnitude higher than the net loss of dissolved and particulate organic carbon from the estuary. This imbalance is attributed to the organic inputs to the estuary through anthropogenic supplies. The bacteriamediated mineralization of organic matter is mainly responsible for the build-up of pCO2 and increased CO2 emission to the atmosphere indicating heterotrophy